Subpopulation Of Tumor Cells Research Articles

Signaling Pathways Associated with Cancer Stem Cells Play a Significant Role in Immunotherapy Resistance

Cancer stem cells (CSCs) are a subpopulation of tumor cells with properties of self-renewal, pluripotency, plasticity, and differentiation, and are associated with various aberrantly stimulated signaling pathways. They are responsible for tumor recurrence, distant metastasis, and drug resistance, thus inducing poor prognosis. Immunotherapy has achieved encouraging results. However, the resistance associated with its clinical application is a persistent problem in clinical and scientific researches. Increasing evidence shows that signaling pathways associated with CSCs mediate immunotherapy resistance. This review highlights the link between them, and focuses on the underlying mechanism so as to provide potential strategies and approaches for the development of new targets against the immune resistance challenge.

A novel circulating tumor cell subpopulation for treatment monitoring and molecular characterization in biliary tract cancer.

In biliary tract cancer (BTC), tissue biopsies to guide treatment are rarely feasible, thus implementing liquid biopsy approaches to improve patient management represents a priority. So far, studies on circulating tumor cells (CTCs) in BTC are insufficient to promote their use in patient clinical management and are limited to EpCAM‐enriched CTCs evaluated with the CellSearch. We applied a single‐cell protocol allowing identification not only of epithelial CTCs (eCTCs), but also of nonconventional CTCs (ncCTCs) lacking epithelial and leukocyte markers, but presenting aberrant genomes as confirmed by copy number alterations and therefore representing a distinct subpopulation of bona fide CTCs. In 41 blood samples longitudinally collected from 21 patients with advanced‐stage BTC, addition of ncCTC to classic eCTC led to a CTC‐positivity increase from 19% to 83%. Patients presenting with at least 1 eCTC/10 ml of blood at baseline prior to treatment start had a significantly shorter median disease‐specific survival (DSS) compared to those lacking eCTCs (9 months vs. 19 months, p = 0.03 by log‐rank test). No differences in DSS were observed according to ncCTC‐positivity, conversely, variations in ncCTC counts during, and at the end of treatment, were associated with the RECIST response supporting their role in treatment monitoring. Moreover, in 88 ncCTCs collected at different times during treatment, unsupervised clustering evidenced segregation of cells by patient's best response, allowing identification of genomic regions possibly involved in resistance mechanisms. The presence of ncCTCs beside eCTCs opens the way to exploiting liquid biopsy for optimizing clinical management in BTC.

Melatonin modifies tumor hypoxia and metabolism by inhibiting HIF-1α and energy metabolic pathway in the in vitro and in vivo models of breast cancer

Breast cancer is the most common cancer among women and has a high mortality rate. Adverse conditions in the tumor microenvironment, such as hypoxia and acidosis, may exert selective pressure on the tumor, selecting subpopulations of tumor cells with advantages for survival in this environment. In this context, therapeutic agents that can modify these conditions, and consequently the intratumoral heterogeneity need to be explored. Melatonin, in addition to its physiological effects, exhibits important anti-tumor actions which may associate with modification of hypoxia and Warburg effect. In this study, we have evaluated the action of melatonin on tumor growth and tumor metabolism by different markers of hypoxia and glucose metabolism (HIF-1α, glucose transporters GLUT1 and GLUT3 and carbonic anhydrases CA-IX and CA-XII) in triple negative breast cancer model. In an in vitro study, gene and protein expressions of these markers were evaluated by quantitative real-time PCR and immunocytochemistry, respectively. The effects of melatonin were also tested in a MDA-MB-231 xenograft animal model. Results showed that melatonin treatment reduced the viability of MDA-MB-231 cells and tumor growth in Balb/c nude mice (p <0.05). The treatment significantly decreased HIF-1α gene and protein expression concomitantly with the expression of GLUT1, GLUT3, CA-IX and CA-XII (p <0.05). These results strongly suggest that melatonin down-regulates HIF-1α expression and regulates glucose metabolism in breast tumor cells, therefore, controlling hypoxia and tumor progression.

EXPRESSION OF CANCER STEM CELLS SURFACE MARKERS IN TONGUE SQUAMOUS CELL CARCINOMA CELL LINES

Cancer stem cells (CSCs) comprise subpopulation of tumor cells associated with cancer initiation, progression, and treatment failures found in several malignancies, including oral squamous cells carcinoma (OSCC). Currently, among the methods employed for detection and isolation of CSCs the most used is flow cytometry immunophenotyping. The expression of surface markers for CSCs in SCC-9 cells, derived from tongue OSCC, has not been described in the literature. Objective: To identify and compare the expression of cell surface markers associate to CSCs in the SCC9 ZsGreen and its metastatic derivative SCC9 ZsGreen LN1 cells. Methods: The CSC subpopulations in cultured SCC9 ZsGreen and SCC9 ZsGreen LN1 were identified by flow cytometry using the following surface markers: CD44 standard (and its isoforms, CD44 v3, and CD44 v6), CD133, CD326, CD24, and CD271. Results: SCC9 ZsGreen cells were significantly more positive for CD44, CD133, and CD271 while SCC9 ZsGreen LN1 expressed more CD326. The positivity for CD24 e CD44 v3 was also higher in SCC9 ZsGreen LN1, however, without statistical significance. Conclusions: The 2 OSCC cell lines presented distinct patterns of cancer stem cells surface markers. Further experiments will be needed to better characterize the CSCs populations present in SCC9 and SCC9 ZsGreen LN1 cell lines. (FAPESP 14/20832-3).

Abstract C08: SM08502, a novel, small-molecule CDC-like kinase (CLK) inhibitor, demonstrates activity against cancer stem cell (CSC)-enriched pancreatic cancer cells and suppresses stemness in vitro

Abstract Cancer stem cells (CSCs) are a rare subpopulation of quiescent tumor cells with the ability to self-renew and form new tumors (stemness) that have been identified in many tumor types, including pancreatic cancer (PC). The presence of CSCs in PC tumors may contribute to chemotherapy resistance and relapse. The Wnt signaling pathway is a highly conserved developmental pathway that has been implicated in the maintenance and survival of CSCs. Aberrant activation of Wnt signaling is common in PC where it may functionally support cell proliferation and tumor-forming capacity; therefore, this pathway is a therapeutic target of interest. SM08502 is a novel, small-molecule pan-CLK inhibitor that has been shown to potently inhibit Wnt pathway activity in preclinical studies. The purpose of these studies was to test the hypothesis that SM08502 could impair CSC viability and stemness in PC cell lines. CSC-enriched tumor spheres were generated by culturing Panc1 cells in nonadherent conditions in which most cells lacking stemness undergo anoikis (programmed cell death). These CSC-enriched Panc1 (Panc1-CSC) cell cultures were analyzed for stemness marker expression via FACS and qPCR to validate the enrichment protocol. The effect of SM08502 on spheroid formation and viability was assessed in comparison to salinomycin and napabucasin as positive controls for CSC inhibition. Inhibition of CSCs within parental PC lines (Capan-1, HPAFII, and Panc1) was assessed by 4-day pretreatment of cells in culture with DMSO or SM08502 and a 4-day recovery period followed by plating 1 or 10 cells/well in 96-well plates under nonadherent conditions and quantifying spheroid formation after 24 days. Anoikis-mediated CSC enrichment increased the percentage of cells expressing the stem cell surface protein marker CXCR4 and increased expression of multiple stemness-related genes. Treatment with either positive control compounds or SM08502 inhibited spheroid formation and decreased the viability of the Panc1-CSC cells. Notably, SM08502 was more potent by EC50 than either salinomycin or napabucasin in the cell viability assay. Expression analyses indicated that SM08502 significantly reduced stemness-related gene expression in Panc1-CSC cultures, including CD24, LGR4, and VDR (p<0.01 vs DMSO). In addition, treatment of Capan-1, HPAFII, and Panc1 cells with SM08502 strongly impaired their ability to form spheres by 8- to 12-fold vs. DMSO, indicating that CSCs within these cell line populations are sensitive to treatment with SM08502. In summary, SM08502 demonstrated anti-CSC activity against PC and appeared more potent than known CSC-inhibiting compounds. By depleting CSCs and reducing stemness in tumors, SM08502 can potentially address relapse and treatment resistance in PC. A phase 1 study assessing safety, tolerability, and pharmacokinetics of SM08502 in subjects with advanced solid tumors is ongoing (NCT03355066). Citation Format: Carine Bossard, Nathalia Cruz, Brian Eastman, Chi-Ching Mak, Sunil KC, Betty Tam, Timothy Phalen, Steven Cha. SM08502, a novel, small-molecule CDC-like kinase (CLK) inhibitor, demonstrates activity against cancer stem cell (CSC)-enriched pancreatic cancer cells and suppresses stemness in vitro [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr C08.

Elucidating the roles of ASPM isoforms reveals a novel prognostic marker for pancreatic cancer.

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers worldwide. Late diagnosis, desmoplastic tissue and intrinsic resistance to therapy are among the main reasons for its aggressive phenotype. In addition, it is now appreciated that cancer stem cells-a rare subpopulation of tumor cells highly resistant to therapy-are crucial players in PDAC initiation, progression and resistance to therapy. In a recent article in The Journal of Pathology, Hsu et al elucidated the specific roles of abnormal spindle-like, microcephaly-associated protein (ASPM) isoforms in PDAC. The authors reported that ASPM isoform I (ASPM-iI) is mainly expressed in the cytoplasm of PDAC cells. Its expression is associated with the Wnt signaling pathway, which promotes stemness and maintains the cancer stem cell niche. Clinically, expression of ASPM-iI correlates with poor survival in PDAC patients. Thus, this study revealed a novel prognostic marker as well as a potential therapeutic target for PDAC. © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Abstract A132: Characterization of intratumoral heterogeneity in drug sensitivity and non-cell autonomous mechanisms of drug resistance using subclonal cell populations derived from a single breast cancer cell line

Abstract Intratumoral heterogeneity impacts both tumor progression and drug sensitivity. While intratumoral genetic heterogeneity has been extensively described, there is still little understanding of the extent of heterogeneity in drug sensitivity within a single tumor, the intra tumor dynamics of different cell populations during anti-cancer compound treatment, and the role of non-cell autonomous mechanism in drug resistance. The objective of this study is to characterize heterogeneity in drug sensitivity within a model for human breast cancer, identify interactions between clonal population influencing drug sensitivity, and use this to model the dynamics of sub populations in a tumor during anti-cancer compound treatment. We have characterized 31 subclonal cell populations (SCPs) that were generated by single cell cloning of the triple-negative breast cancer cell line MDA-MB-468. These SCPs display considerable phenotypic and molecular heterogeneity with respect to morphology, proliferation rate, RNA expression and tumorigenicity in mice. To examine the extent of heterogeneity in drug sensitivity, we designed and screened a 200-small molecule compound library in 24 SCPs and the parental cell line. We observed considerable heterogeneity in drug sensitivity and selected 36 compounds for validation in the SCPs that expressed the greatest range of sensitivity (determined by IC50). To investigate whether interactions between clonal population can influence drug sensitivity heterogeneously responsive subclonal cell lines were transduced with lentiviruses encoding for the H2B-GFP or H2B-RFP fusion protein and then cocultured in the absence or presence of different compounds. We observed shifts in drug sensitivity for SCPs that were cocultured with differentially responsive clones. Examples include SCPs 19 and 27 two highly sensitive populations that were protected by the presence of less sensitive SCPs when under gemcitabine treatment, resulting in IC50-values that were 20-fold higher then when cultured alone. RNA-sequencing and RPPA analysis will be used to characterize this non-cell autonomous mechanism of resistance and the relationship with identified transcriptional programs or genes which expression correlates with drug sensitivity. We are also generating and will evaluate predictive models for drug combination using the SCP drug sensitivity profiles. The results of this study show that there is considerable heterogeneity in drug sensitivity among clonal subpopulations derived from a single cancer cell line. Ongoing experiments will provide insight into the effect of drug combinations and unique treatment schedules on distinct tumor cell subpopulations and drug sensitivity within heterogenous mixtures. Moreover, we will be able to test for and investigate non-cell autonomous modes of drug resistance, which may guide the development of new drug combination treatments or schedules. Citation Format: Chandler M Friend, Joan S Brugge, Hendrik J Kuiken, Steven M Corsello, Christopher C Mader. Characterization of intratumoral heterogeneity in drug sensitivity and non-cell autonomous mechanisms of drug resistance using subclonal cell populations derived from a single breast cancer cell line [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr A132. doi:10.1158/1535-7163.TARG-19-A132

Ten patients with high-grade transformation of acinic cell carcinomas: Expression profiling of β-catenin and cyclin D1 is useful

Conventional acinic cell carcinoma (CACC) represents a prototypical low-grade salivary malignancy. Rarely, acinic cell carcinoma (ACC) can demonstrate aggressive features (zones of necrosis, apoptosis, varying nuclear atypia) warranting classification as “ACC with high-grade transformation” (HGT-ACC) or “dedifferentiated” ACC. This study reports ten new cases of HGT-ACC. There is potential for subtlety in recognizing high-grade transformation and distinguishing discrete nodules of necrosis from cytology aspiration changes. We compared immunohistochemical (IHC) profiles, specifically β-catenin (bCAT) and cyclin D1 expression, which have been touted as potentially helpful in this context. We quantified morphology (primary axis nucleus, nuclear area and perimeter) in HGT-ACC and CACC.Clinical outcome is known for eight HGT-ACC patients; three patients developed locoregional or distant metastases, five remained disease-free. Nine of ten HGT-ACC expressed strong, diffuse, membranous bCAT. CACC demonstrated lower intensity of membranous bCAT expression. Strong, diffuse nuclear cyclin D1 was seen in five of ten HGT-ACC whereas no CACC demonstrated cyclin D1 with distribution greater than 50 %. The quantified nuclear morphologic features of CACC and HGT-ACC demonstrated overlapping means values. Maximum values for nuclear primary axis, area, and perimeter were greater for HGT-ACC versus CACC, corresponding to a subpopulation of larger tumor cells in HGT-ACC.The poor outcome associated with HGT-ACC justifies its recognition, which should alter surgical approach with respect to elective neck dissection or possible facial nerve sacrifice. With respect to ancillary IHC studies, strong, diffuse membranous bCAT expression, with or without strong nuclear cyclin D1 ≥ 50 % distribution or Ki67 index ≥ 25 % supports this diagnosis.

Targeting histone deacetylase SIRT1 selectively eradicates EGFR TKI-resistant cancer stem cells via regulation of mitochondrial oxidative phosphorylation in lung adenocarcinoma

Lung adenocarcinoma (LAD) is a human malignancy successfully treated with the tyrosine kinase inhibitor (TKI) gefitinib; however, the enrichment of therapy resistant cancer stem cells (CSCs) in such patients is assumed to be a source of treatment failure. Evaluation of LAD cell populations treated with the TKI inhibitor gefitinib identified unique aspects of a subpopulation of tumor cells exhibiting stem-like properties and mitochondria-specific metabolic features along with their reliance on sirtuin 1 (SIRT1) for survival advantage. This addiction to bioenergetic metabolism in LAD treated with EGFR-targeted therapy suggests that mitochondrial targeting should be synthetically lethal using established cytotoxic therapies. Accordingly, loss of the phenotype present in resistant CSC clones either by targeting the energy metabolism with tigecycline, a mitochondrial DNA-translation inhibitor, or tenovin-6 (TV-6), a SIRT1 inhibitor, inhibited their dependency on mitochondrial oxidative phosphorylation (mtOXPHOS) and sensitized them for a more pronounced and long-lasting TKI therapeutic effect. The results specifically demonstrated that combined therapy with TV-6 and gefitinib resulted in tumor regression in xenograft mouse models, whereas administration of a single agent showed no such efficacy. Importantly, combined treatment with TV-6 also decreased the effective dose of gefitinib necessary for treatment response. Clinical analysis demonstrated that high-profile SIRT1 and mtOXPHOS proteins were associated with recurrence and poor prognosis in LAD patients. These observations support the CSC hypothesis for cancer relapse and advocate use of mitochondria-targeting inhibitors as part of combinatorial therapy in a variety of clinical settings, as well as for reducing first-line TKI dosage in LAD patients.

Avoidance of apoptotic death via a hyperploid salvage survival pathway after platinum treatment in high grade serous carcinoma cell line models.

The alkylating agent platinum is first-line chemotherapy treatment for high-grade serous carcinomas (HGSC) of tubal-ovarian origin. Platinum compounds cause DNA damage and induce apoptotic cell death in the bulk tumor population. However, subpopulations of tumor cells may exhibit diverging behaviors from the bulk tumor due to an alternate stress response that diverts tumor cells from apoptotic death. In this study, we identified a salvage survival pathway in which G2-arrested tumor cells bypassed apoptosis and progressed through aberrant mitotic events to then emerge as a distinct subpopulation of viable large hyperploid cells but with uncertain long-term propagation potential. Platinum-induced large hyperploid cells were flow sorted and showed rare regrowth capacity as compared to their more proficiently regenerating non-hyperploid counterparts. However, detailed time-lapse microscopy provided direct evidence that these hyperploid cells were mitotically active and could divide successfully to produce viable daughter cells. The hyperploid survival response was observed across different cell lines and utilization of this survival pathway was dependent on the strength of the G2-M checkpoint. Conceivably, this salvage survival strategy may contribute to increased genomic diversity of the regenerating tumor cell line through a coupled hyperploidization and de-polyploidization process that may be relevant for drug resistance.

Unravelling Heterogeneity of Stem and Progenitor Cells in Myeloid Neoplasms Through Single Cell Multi-omics

Intratumoural heterogeneity (ITH) underlies many of the challenges we face in cancer medicine, including therapy-resistance, disease progression/evolution and relapse after seemingly effective therapy. Distinct tumour cell subpopulations selectively evade therapy and drive disease-progression and technologies that reveal key aspects of ITH are therefore critical for the application of precision cancer medicine. Although bulk genomic analysis has without question provided many insights into genetic ITH, this approach faces a number of fundamental limitations: ITH in cancer occurs at many levels, not restricted to genetics (mutations) but also other factors, such as presence of cancer stem cells in some tumours. Furthermore, bulk genomic analysis reveals patterns of somatic mutations, but not their molecular consequences within distinct (and therapy-resistant) cancer subclones. Whilst many of the scientific questions relating to ITH have remained the same over many decades, our ability to address these questions has advanced dramatically not least because of advances in technology. Ultimately, as the unit of evolution and clonal selection by therapy in cancer is the cell, techniques that resolve heterogeneity at the single-cell level are ideally placed to unravel ITH and provide entirely new insights into cancer biology, with enormous potential to accelerate the development of new approaches to improve outcomes for patients. However, the lack of coverage across key mutation hotspots when studying cancers using single-cell RNA-sequencing techniques has precluded the correlation of genetic and transcriptional readouts from the same single cell, limiting their application to the study of tumors. To overcome such limitation, we developed TARGET-seq, a single cell multi-omic method for the high-sensitivity detection of mutations within single cells in parallel with whole transcriptome analysis. TARGET-seq achieved extremely low allelic dropout rates, allowing resolution of clonal hierarchies with over 98% accuracy, while obtaining unbiased high quality transcriptomes from the same single cell. We have applied TARGET-seq to the study of over ten thousand haematopoietic stem and progenitor cells (HSPCs) from JAK2-mutant myeloproliferative neoplasms. This analysis revealed a high degree of genetic heterogeneity, identifying both linear and branching patterns of clonal evolution. At the transcriptome level different genetic subclones showed distinct transcriptional signatures, indicating that each of them was molecularly distinct. Wild-type cells from MPN patients also showed disrupted gene expression as compared to cells from normal donors, upregulating molecular pathways associated with inflammation (TNFα, TGFβ and IFN signalling). This suggests cell-extrinsic effects disrupting gene expression in non-mutant cells, which has been shown to have prognostic significance and might underlie therapy response. Moreover, TARGET-seq analysis allowed us to identify putative biomarkers of JAK2V617F mutant cells, including novel therapeutic targets to selectively eradicate JAK2-mutant cells and importantly, potential candidates for antibody-based immunotherapy. Analysis of samples from MPN patients undergoing disease transformation to Acute Myeloid Leukemia (sAML) revealed striking patterns of clonal evolution in different immunophenotypically-defined cell types. We identified pre-leukemic and leukemic subclones emerging from hematopoietic stem cells rather than more mature progenitors, in contrast to evolution patterns in de novo AML, which might indicate different cancer stem cell reservoirs. In summary, TARGET-seq allowed us to identify distinct and biologically relevant molecular signatures of different genetic subclones of HSPCs in myeloproliferative neoplasms. TARGET-seq could also be broadly applied to the study of other types of tumours, providing a powerful tool for biomarker and therapeutic target discovery for precision medicine. Disclosures Mead: Bristol Myers-Squibb: Consultancy; Pfizer: Consultancy; Novartis: Consultancy, Honoraria, Other: Travel/accommodation expenses, Research Funding, Speakers Bureau; CTI: Honoraria, Research Funding; Celgene: Consultancy, Research Funding.

STEM-09. INTRINSIC TUMOR PLASTICITY IN GLIOBLASTOMA ALLOWS FOR RECREATION OF STEM LIKE-STATES AND EFFICIENT TUMOR CELL ADAPTATION TO NEW MICROENVIRONMENTS

Abstract BACKGROUND Cellular heterogeneity is a hallmark of numerous cancer types, including Glioblastoma (GBM). Cancer stem cells (CSC) have been accounted for the generation of phenotypic heterogeneity and tumor progression in GBM. Recent data, however, suggest that CSCs may not represent a stable entity and intrinsic plasticity plays a key role in tumor adaptation to changing microenvironments. The question arises whether CSCs are a defined subpopulation of GBM or whether they represent a cellular state that any cancer cell can adopt. METHODS We interrogated intra-tumoral phenotypic heterogeneity at the single cell transcriptomic and proteomic level in GBM biopsies, patient-derived stem-like cultures and orthotopic xenografts (PDOXs). Tumor cell subpopulations, classified based on their expression of four proposed stem cell markers (CD133, CD15, A2B5 and CD44), were FACS isolated and functionally characterized under various microenvironmental conditions. Mathematical Markov modelling was applied to calculate state transitions. RESULTS GBM patient biopsies, PDOXs and stem-like cell cultures displayed remarkable stem cell-associated intra-tumoral heterogeneity. However independent of marker expression, all analysed tumor subpopulations carried stem-cell properties and recreated phenotypic heterogeneity. Mathematical modeling revealed a different propensity in reforming heterogeneity over time, which was independent of the proliferation index but linked to in vivo tumorigenic potential. Although GBM subpopulations varied in their potential to adapt to new environments, all were able to reach a steady state microenvironment-specific equilibrium. CONCLUSIONS Our results suggest that phenotypic heterogeneity in GBM results from intrinsic plasticity allowing tumor cells to adapt to changing microenvironmental conditions. Cellular states are non-hierarchical, reversible and occur via stochastic state transitions, striving towards a microenvironment-instructed equilibrium. Our data provides evidence that CSCs do not represent a defined clonal entity, but rather a cellular state determined by environmental conditions, which has implications for the design of treatment strategies targeting CSC-like states.

TMIC-32. PARALLEL SINGLE CELL NUCLEOSOME OCCUPANCY AND RNA SEQUENCING ON RECURRENT GBM

Abstract Nearly all patients diagnosed with Glioblastoma (GBM) will experience a fatal recurrence of the tumor. Thought to be in part driven by immense tumor heterogeneity it is important to explore the small subpopulations of tumor cells with in depth single cell sequencing pre and post therapy in order to understand recurrence. To this end, we created an experimental in vivo pipeline that allows us profile not only gene expression changes during therapy, but also epigenetic shifts due to methylation across the genome at the single cell level from a single tumor. Single Cell NomE-Seq libraries were created and correctly identified characteristic CTCF binding regions within DNase1 hypersensitivity regions when compared back to representative encode data sets. Primary tumors analyzed by single cell RNA sequencing showed enrichment for on average 5 significant principle components (St. Dev >2 verified by Elbow Plot). Comparatively, recurrent temozolomide (TMZ) exposed tumors averaged 10 significant principle components (St. Dev >2 verified by Elbow Plot) suggesting TMZ therapy causes tumors to diversify their gene expression profiles. For direct comparison samples were merged into a continuous data set and dimensional analysis with TSNE reduction (15 dimensions used) identified 6 unique clusters, with one cluster being over-represented by cells from recurrent, TMZ exposed mice. Gene Ontology analysis on expression values contained within in this cluster demonstrated significant enrichment for ribosome biogenesis/ribosomal structure, (p=2.87e-17) and mRNA catabolic processes (p=2.47e-30). Further, comparison to a similar data set gathered using cells in vitro culture conditions demonstrates superior intraturmoral heterogeneity from cells isolated freshly from the brains of mice as opposed to tissue culture, indicating the effectiveness of our model for assaying heterogeneity. Ultimately, these data illuminate possible new mechanisms for TMZ induced ribosomal modifications underlying intraturmoral heterogeneity in GBM and provide an expandable technique for further experimentation.

STEM-27. LEVERAGING FUNCTIONAL GENETIC DEPENDENCIES IN TREATMENT-REFRACTORY GLIOBLASTOMA

Abstract As the most common primary brain tumor in adults causing death, Glioblastoma (GBM) remains a therapeutic challenge. Unchanged for almost two decades, standard therapy is ineffective at preventing disease relapse with a median patient survival of < 15 months. Stem cell-like subpopulations of tumor cells, known as brain tumor initiating cells (BTICs), evade standard therapy and lead to relapse. Whereas previous studies largely focus on pre-treatment primary GBM (pGBM), we conducted a panel of genome-wide CRISPR-Cas9 gene knockout screens to determine modulators of treatment resistance and de novo genetic vulnerabilities arising at disease recurrence. Using our in vitro model of conventional therapy, we identified genes modulating sensitivity and resistance to Temozolomide and/or radiation therapy in patient-derived pGBM BTICs. Genes modulating sensitivity belong to Fanconi anaemia nuclear complex, interstrand cross link repair, and regulation of stem cell maintenance and differentiation. Following in vitro validation of gene knockouts conferring treatment sensitization in multiple pGBM BTIC lines, we continued to conduct the first genome-wide CRISPR-Cas9 screens in patient-derived rGBM BTICs. Focusing on genetic vulnerabilities arising de novo at disease relapse, we introduce the context-specific role of protein tyrosine phosphatase 4A2 (PTP4A2) in rGBM. Genetic knockout or small molecule targeting of PTP4A2 leads to a context-specific vulnerability of rGBM self renewal capacity and in vivo tumorigenecity. To continue our analysis of treatment-refractory GBM and overcome intertumoral heterogeneity, we conducted genome-wide CRISPR-Cas9 gene knockout screens and whole cell proteomics on patient-matched pGBM and rGBM BTICs. With >1000 differentially essential genes, combined functional genetic and proteomic analyses implicates genes involved in mRNA splicing, nucleotide metabolism, and activation of gene expression by sterol regulatory element-binding protein. Together, our functional genetic approach elucidates novel genes regulating treatment resistance and disease recurrence in GBM.

COMP-12. SINGLE-CELL TRANSCRIPTOME PROFILING OF GBM TISSUE ACUTE SLICE CULTURES FOR PERSONALIZED DRUG SCREENING

Abstract Glioblastoma (GBM) is the most common and malignant type of primary brain tumor, and more effective treatment options are needed. Both inter- and intratumoral heterogeneity present major challenges to the application of targeted therapies in GBM. Therefore, precision medicine approaches to GBM would benefit significantly from the ability to predict drugs or drug combinations that target specific subpopulations of tumor cells. Model systems, such as adherent cell lines, neurospheres, patient-derived xenografts (PDXs), and patient-derived organoids, have been reported as platforms for drug screening and accessing drug responses. However, these models do not recapitulate the full heterogeneity of GBM tissue, lack key components of the tumor microenvironment or take weeks to months to establish, which limits the predictive power of drug response assays or delays clinical decision-making. To address these limitations, we are combining ex vivo slices of intact, patient-derived GBM tissue with single-cell RNA-seq (scRNA-seq) for small-scale drug screening and assessment of patient- and cell type-specific drug responses. We generated slices from both preclinical mouse glioma models and surgical specimens from GBM patients and showed that acute slices preserved both the tumor heterogeneity and tumor microenvironment observed in scRNA-seq of cells directly isolated from tumor tissue. To test drug responses, we treated tissue slices from GBM mouse models and five different patients with six drugs for 18hr. By performing scRNA-Seq and analyzing transcriptional profiles of treated and untreated control slices, we identified drug-induced transcriptional responses in specific subpopulations of tumor cells, patient-specific drug sensitivities, and drug effects conserved in both mouse and human tumors. The GBM tissue slices were generated immediately following surgical resection, and experiments were completed within 24 hours. With these features, our method is attractive for rapidly accessing cell type- and patient-specific drug responses and has potential for preclinical drug screening and guiding personalized treatment for GBM.

Cancer stem cell theory: Are we moving past the mist?

Cancer stem cells (CSC) are a subpopulation of tumor cells that have superior capacities of self-renewal, metastatic dissemination, and chemoresistance. These characteristics resemble, to some extent, the outcome of certain biological processes, including epithelial-mesenchymal transition (EMT), autophagy, and cellular stress response. Indeed, it has been shown that the stimuli that induce these processes and CSC are overlapping, and CSC and tumor cells that underwent EMT or autophagy are much alike. However, as the cross talk between CSC, EMT, autophagy, and cellular stress is further explored, these processes are also found to have an opposing role in CSC, depending on the condition and status of cells. This contextual effect is likely due to overwhelming reliance on CSC markers for their identification, and/or discrepancies in recognition of CSC as a particular cell population or cellular state. In this review, we summarize how EMT, autophagy, and cellular stress response are tied or unwound with CSC. We also discuss the current view of CSC theory evolved from the emphasis of heterogenicity and plasticity of CSC.

GPR56 Drives Colorectal Tumor Growth and Promotes Drug Resistance through Upregulation of MDR1 Expression via a RhoA-Mediated Mechanism

Drug resistance continues to be a major obstacle of effective therapy for colorectal cancer, leading to tumor relapse or treatment failure. Cancer stem cells (CSC) or tumor-initiating cells are a subpopulation of tumor cells which retain the capacity for self-renewal and are suggested to be implicated in drug resistance. LGR5 is highly expressed in colorectal cancer and marks CSCs that drive tumor growth and metastasis. LGR5(+) CSCs cells were shown to interconvert with more drug-resistant LGR5(-) cancer cells, and treatment with LGR5-targeted antibody-drug conjugates (ADC) eliminated LGR5(+) tumors, yet a fraction of LGR5(-) tumors eventually recurred. Therefore, it is important to identify mechanisms associated with CSC plasticity and drug resistance in order to develop curative therapies. Here, we show that loss of LGR5 in colon cancer cells enhanced resistance to irinotecan and 5-fluorouracil and increased expression of adhesion G-protein-coupled receptor, GPR56. GPR56 expression was significantly higher in primary colon tumors versus matched normal tissues and correlated with poor survival outcome. GPR56 enhanced drug resistance through upregulation of MDR1 levels via a RhoA-mediated signaling mechanism. Loss of GPR56 led to suppression of tumor growth and increased sensitivity of cancer cells to chemotherapy and monomethyl auristatin E-linked anti-LGR5 ADCs, by reducing MDR1 levels. These findings suggest that upregulation of GPR56 may be a mechanism associated with CSC plasticity by which LGR5(-) cancer cells acquire a more drug-resistant phenotype. IMPLICATIONS: Our findings suggest that targeting GPR56 may provide a new strategy for the treatment of colorectal cancer and combatting drug resistance.

Quantitative Spatial Analysis of Metabolic Heterogeneity Across in vivo and in vitro Tumor Models.

Metabolic preferences of tumor cells vary within a single tumor, contributing to tumor heterogeneity, drug resistance, and patient relapse. However, the relationship between tumor treatment response and metabolically distinct tumor cell populations is not well-understood. Here, a quantitative approach was developed to characterize spatial patterns of metabolic heterogeneity in tumor cell populations within in vivo xenografts and 3D in vitro cultures (i.e., organoids) of head and neck cancer. Label-free images of cell metabolism were acquired using two-photon fluorescence lifetime microscopy of the metabolic co-enzymes NAD(P)H and FAD. Previous studies have shown that NAD(P)H mean fluorescence lifetimes can identify metabolically distinct cells with varying drug response. Thus, density-based clustering of the NAD(P)H mean fluorescence lifetime was used to identify metabolic sub-populations of cells, then assessed in control, cetuximab-, cisplatin-, and combination-treated xenografts 13 days post-treatment and organoids 24 h post-treatment. Proximity analysis of these metabolically distinct cells was designed to quantify differences in spatial patterns between treatment groups and between xenografts and organoids. Multivariate spatial autocorrelation and principal components analyses of all autofluorescence intensity and lifetime variables were developed to further improve separation between cell sub-populations. Spatial principal components analysis and Z-score calculations of autofluorescence and spatial distribution variables also visualized differences between models. This analysis captures spatial distributions of tumor cell sub-populations influenced by treatment conditions and model-specific environments. Overall, this novel spatial analysis could provide new insights into tumor growth, treatment resistance, and more effective drug treatments across a range of microscopic imaging modalities (e.g., immunofluorescence, imaging mass spectrometry).

Mathematical model of hypoxia and tumor signaling interplay reveals the importance of hypoxia and cell-to-cell variability in tumor growth inhibition

BackgroundHuman tumor is a complex tissue with multiple heterogeneous hypoxic regions and significant cell-to-cell variability. Due to the complexity of the disease, the explanation of why anticancer therapies fail cannot be attributed to intrinsic or acquired drug resistance alone. Furthermore, there are inconsistent reports of hypoxia-induced kinase activities in different cancer cell-lines, where increase, decreases, or no change has been observed. Thus, we asked, why are there widely contrasting results in kinase activity under hypoxia in different cancer cell-lines and how does hypoxia play a role in anti-cancer drug sensitivity?ResultsWe took a modeling approach to address these questions by analyzing the model simulation to explain why hypoxia driven signals can have dissimilar impact on tumor growth and alter the efficacy of anti-cancer drugs. Repeated simulations with varying concentrations of biomolecules followed by decision tree analysis reveal that the highly differential effects among heterogeneous subpopulation of tumor cells could be governed by varying concentrations of just a few key biomolecules. These biomolecules include activated serine/threonine-specific protein kinases (pRAF), mitogen-activated protein kinase kinase (pMEK), protein kinase B (pAkt), or phosphoinositide-4,5-bisphosphate 3-kinase (pPI3K). Additionally, the ratio of activated extracellular signal-regulated kinases (pERK) or pAkt to its respective total was a key factor in determining the sensitivity of pERK or pAkt to hypoxia.ConclusionThis work offers a mechanistic insight into how hypoxia can affect the efficacy of anti-cancer drug that targets tumor signaling and provides a framework to identify the types of tumor cells that are either sensitive or resistant to anti-cancer therapy.

Heterogeneity and Plasticity of Human Breast Cancer Cells in Response to Molecularly-Targeted Drugs.

Non-responsive subpopulation of tumor cells, and acquired resistance in initially responsive cells are major challenges for cancer therapy with molecularly-targeted drugs. While point mutations are considered the major contributing factor to acquired resistance, in this study we explored the role of heterogeneity and plasticity of selected human breast cancer cell lines (MDA-MB-231, MDA-MB-468, and AU565) in their initial and adjusted response, respectively, to ruxolitinib, everolimus, and erlotinib. After determination of lethal concentration for 50% cell death (LC50), cells were exposed to selected drugs using three different approaches: single exposure to 4 × LC50 and collection of surviving cells, multiple exposures to 1.5 × LC50 and monitoring the surviving population, and exposure to gradually increasing concentrations of selected drugs (range of concentrations equivalent to 10% of LC50 to 1.5 × LC50). Surviving cells were studied for adjustments in expression level of selected proteins using quantitative PCR and Western Blot. Our data indicated overexpression of a variety of proteins in resistant populations, which included cell membrane receptors EGFR and HER2, anti-apoptotic proteins Bcl-2 and BIRC8, and other proteins involved in cell signaling (e.g., Akt1, MAPK7, and RPS6KA5). Silencing the identified alternative proteins via siRNA resulted in significant drop in the LC50 of the selected molecularly-targeted drugs cells resistant to ruxolitinib (via targeting Akt), everolimus (via targeting EGFR, MAPK7, RPS6KA5, and HER2), and erlotinib (via silencing Bcl2 and BIRC8). Our data indicates that targeting well-selected alternative proteins could potentially sensitize the resistant cells to the effect of the molecularly-targeted treatment.